Automatic Implementation of Neural Networks through Reaction Networks -- Part I: Circuit Design and Convergence Analysis

Information processing relying on biochemical interactions in the cellular environment is essential for biological organisms. The implementation of molecular computational systems holds significant interest and potential in the fields of synthetic biology and molecular computation. This two-part article aims to introduce a programmable biochemical reaction network (BCRN) system endowed with mass action kinetics that realizes the fully connected neural network (FCNN) and has the potential to act automatically in vivo. In part I, the feedforward propagation computation, the backpropagation component, and all bridging processes of FCNN are ingeniously designed as specific BCRN modules based on their dynamics. This approach addresses a design gap in the biochemical assignment module and judgment termination module and provides a novel precise and robust realization of bi-molecular reactions for the learning process. Through equilibrium approaching, we demonstrate that the designed BCRN system achieves FCNN functionality with exponential convergence to target computational results, thereby enhancing the theoretical support for such work. Finally, the performance of this construction is further evaluated on two typical logic classification problems

Coalescence modeling and experimental validation of sintering of thermoplastic polyamide fibers

In order to study the coalescence mechanisms of thermoplastic polymer powders, a 2D mathematical model has been established based on Frenkel, Eshelby and Pokluda’s model. Sintering experiments have been carried out by using two polyamide fibers that can be considered as infinite cylinders with its length much larger than the diameter. 2D mathematical model has been validated through comparison with results of sintering experiments as well as Constrained Natural Element Method (C-NEM) coalescence simulation. This consistence shows that the proposed coalescence model and experimental results can provide a reference for the numerical simulation of sintering process

Enabling urban-scale energy modelling: a new spatial approach

Urban-scale energy modelling provides an ideal tool for studying non-domestic energy consumption and emissions reduction at the community level. In principle, an approach based on the characteristics of individual commercial premises and buildings is attractive, but it poses a number of challenges, the most immediate of which is deciding precisely what to model. For a range of reasons connected with their self-contained nature, individual non-domestic buildings would ideally be selected. However, the main information sources available - digital mapping and business taxation data - are not based on 'buildings' and do not use the concept, thus making an automated approach problematic. At the same time, manual identification of the distinct buildings in a city is not a practical proposition because of the numbers involved. The digital mapping and business taxation data are brought together in the Local Land and Property Gazetteer (LLPG). An analysis of the relationships between the relevant elements, namely building polygons and premises attracting business taxation, allowed a unit to be defined that matches the definition of a 'building' in most circumstances and can be applied without the need for human intervention. This novel approach provides a firmer basis for modelling non-domestic building energy at the urban scale

Interference of Cooper quartet Andreev bound states in a multi-terminal graphene-based Josephson junction

In a Josephson junction (JJ), Cooper pairs are transported via Andreev bound states (ABSs) between superconductors. The ABSs in the weak link of multi-terminal (MT) JJs can coherently hybridize two Cooper pairs among different superconducting electrodes, resulting in the Cooper quartet (CQ) involving four fermions entanglement. The energy spectrum of these CQ-ABS can be controlled by biasing MT-JJs due to the AC Josephson effect. Here, using gate tunable four-terminal graphene JJs complemented with a flux loop, we construct CQs with a tunable spectrum. The critical quartet supercurrent exhibits magneto-oscillation associated with a charge of 4e; thereby presenting the evidence for interference between entangled CQ-ABS. At a finite bias voltage, we find the DC quartet supercurrent shows non-monotonic bias dependent behavior, attributed to Landau-Zener transitions between different Floquet bands. Our experimental demonstration of coherent non-equilibrium CQ-ABS sets a path for design of artificial topological materials based on MT-JJs

On the Importance of Electroweak Corrections for Majorana Dark Matter Indirect Detection

Recent analyses have shown that the inclusion of electroweak corrections can alter significantly the energy spectra of Standard Model particles originated from dark matter annihilations. We investigate the important situation where the radiation of electroweak gauge bosons has a substantial influence: a Majorana dark matter particle annihilating into two light fermions. This process is in p-wave and hence suppressed by the small value of the relative velocity of the annihilating particles. The inclusion of electroweak radiation eludes this suppression and opens up a potentially sizeable s-wave contribution to the annihilation cross section. We study this effect in detail and explore its impact on the fluxes of stable particles resulting from the dark matter annihilations, which are relevant for dark matter indirect searches. We also discuss the effective field theory approach, pointing out that the opening of the s-wave is missed at the level of dimension-six operators and only encoded by higher orders.Comment: 25 pages, 6 figures. Minor corrections to match version published in JCA

The Pkn22 Ser/Thr kinase in Nostoc PCC 7120: role of FurA and NtcA regulators and transcript profiling under nitrogen starvation and oxidative stress

International audienceBackground: The filamentous cyanobacterium Nostoc sp. strain PCC 7120 can fix N2 when combined nitrogen is not available. Furthermore, it has to cope with reactive oxygen species generated as byproducts of photosynthesis and respiration. We have previously demonstrated the synthesis of Ser/Thr kinase Pkn22 as an important survival response of Nostoc to oxidative damage. In this study we wished to investigate the possible involvement of this kinase in signalling peroxide stress and nitrogen deprivation. Results: Quantitative RT-PCR experiments revealed that the pkn22 gene is induced in response to peroxide stress and to combined nitrogen starvation. Electrophoretic motility assays indicated that the pkn22 promoter is recognized by the global transcriptional regulators FurA and NtcA. Transcriptomic analysis comparing a pkn22-insertion mutant and the wild type strain indicated that this kinase regulates genes involved in important cellular functions such as photosynthesis, carbon metabolism and iron acquisition. Since metabolic changes may lead to oxidative stress, we investigated whether this is the case with nitrogen starvation. Our results rather invalidate this hypothesis thereby suggesting that the function of Pkn22 under nitrogen starvation is independent of its role in response to peroxide stress. Conclusions: Our analyses have permitted a more complete functional description of Ser/Thr kinase in Nostoc. We have decrypted the transcriptional regulation of the pkn22 gene, and analysed the whole set of genes under the control of this kinase in response to the two environmental changes often encountered by cyanobacteria in their natural habitat: oxidative stress and nitrogen deprivation